A scanning electron microscope (SEM) is know which is configured such that an angle of incidence of a focused electron beam onto a specimen can be varied. Using such SEM, it is possible, for example, to obtain a first image by scanning the specimen with a focused electron beam while an angle of incidence of the beam on the specimen is set to a first value, and to obtain a second image by scanning the same specimen with the electron beam while the angle of incidence is set to a second value different from the first value. From analyzing the two images it is possible to reconstruct a three-dimensional structure of the specimen. The charged particle beam column can include an aberration corrector to compensate aberrations caused by condenser lenses and an objective lens of the charged particle beam column due to high tilted angles of the beam traversing the column including the condenser lenses and objective lens.